Your message dated Mon, 22 Oct 2018 16:51:14 +0000 with message-id <[email protected]> and subject line Bug#911609: fixed in libpdl-io-hdf5-perl 1:0.73-5 has caused the Debian Bug report #911609, regarding libpdl-io-hdf5-perl: FTBFS with HDF5 1.10.3 to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 911609: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=911609 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Source: libpdl-io-hdf5-perl Version: 1:0.73-4 Severity: important Tags: patch -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Hi, libpdl-io-hdf5-perl FTBFS against HDF5 1.10.3 currently in experimental: make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_test -O--parallel make -j5 test TEST_VERBOSE=1 make[1]: Entering directory '/<<PKGBUILDDIR>>' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HDF5.bs blib/arch/auto/PDL/IO/HDF5/HDF5.bs 644 PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t HDF5-DIAG: Error detected in HDF5 (1.10.3) thread 140450522435520: #000: ../../../src/H5Ddeprec.c line 257 in H5Dextend(): unable to extend dataset major: Dataset minor: Unable to initialize object #001: ../../../src/H5Dint.c line 2603 in H5D__set_extent(): dataset has contiguous storage major: Invalid arguments to routine minor: Out of range Error extending dataset in PDL::IO::HDF5::Dataset:set at t/attribPDL.t line 33. # Failed test at t/attribPDL.t line 67. # Looks like you failed 1 test of 13. t/attribPDL.t ..... ... All failures are related to the error above, occuring during dataset creation. As I undertand it, in dataset->set(), the dataset is first created, then extended to store the data. In HDF5 1.10.3, dataset extension now relies on H5D__set_extent() where we have: /* Check if we are allowed to modify the space; only datasets with chunked and external storage are allowed to be modified */ if(H5D_COMPACT == dset->shared->layout.type) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "dataset has compact storage") if(H5D_CONTIGUOUS == dset->shared->layout.type && 0 == dset->shared->dcpl_cache.efl.nused) HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "dataset has contiguous storage") The attached patch fixes the failing tests by creating the datasets with the option 'unlimited' to workaround the problem. Thanks, _g. - -- System Information: Distributor ID: PureOS Description: PureOS GNU/Linux 8 Release: 8 Codename: green Architecture: x86_64 Kernel: Linux 4.14.0-3-amd64 (SMP w/4 CPU cores) Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE=fr_FR.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEoJObzArDE05WtIyR7+hsbH/+z4MFAlvN1GQACgkQ7+hsbH/+ z4OGVQf8CMu/FyaZn35Z63qmZ6fKGS+ba24kifwHexnAnbDCtU16V8wO/oykgJH0 qbdztqGexfRK6rrYcdb1tC2/P790CrPaTREUwMWqyYudOQpA24uX6SqaH4W2MbYX KYe1YBG5KfaN5m7tUiAoMc5DtZOreo5jk/++77g9Ygx9BMm8LxjN9pVab41GD3VW 4ACyJFLt9Q6Iv2SC0jq91Ssb1+N3kbDT8Pm8ty645sMgoJhWxDV0wWroZe0cPAx8 ZbgXZ2vYf7k2TH5uLbblqvwgsngMB/uE+nwxvFqWXeR3wOqiJqSjXCdmeughqXZn 9XngiQEzBC+ihYL4LTnYkJStBarW6g== =bbcn -----END PGP SIGNATURE-----diff -Nru libpdl-io-hdf5-perl-0.73/debian/changelog libpdl-io-hdf5-perl-0.73/debian/changelog --- libpdl-io-hdf5-perl-0.73/debian/changelog 2018-07-22 19:38:40.000000000 +0200 +++ libpdl-io-hdf5-perl-0.73/debian/changelog 2018-10-22 15:30:22.000000000 +0200 @@ -1,3 +1,10 @@ +libpdl-io-hdf5-perl (1:0.73-4.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * New patch to support HDF5-1.10.3 + + -- Gilles Filippini <[email protected]> Mon, 22 Oct 2018 15:30:22 +0200 + libpdl-io-hdf5-perl (1:0.73-4) unstable; urgency=medium * Team upload. diff -Nru libpdl-io-hdf5-perl-0.73/debian/patches/hdf5-1.10.3.patch libpdl-io-hdf5-perl-0.73/debian/patches/hdf5-1.10.3.patch --- libpdl-io-hdf5-perl-0.73/debian/patches/hdf5-1.10.3.patch 1970-01-01 01:00:00.000000000 +0100 +++ libpdl-io-hdf5-perl-0.73/debian/patches/hdf5-1.10.3.patch 2018-10-22 15:02:03.000000000 +0200 @@ -0,0 +1,79 @@ +Index: libpdl-io-hdf5-perl-0.73/t/attribPDL.t +=================================================================== +--- libpdl-io-hdf5-perl-0.73.orig/t/attribPDL.t ++++ libpdl-io-hdf5-perl-0.73/t/attribPDL.t +@@ -30,7 +30,7 @@ my $group=$hdf5->group('Radiometric info + + # Store a dataset + my $dataset=$group->dataset('SP_BT'); +-$dataset->set($bt); ++$dataset->set($bt, unlimited => 1); + + # Store a scalar and pdl attribute + $dataset->attrSet('UNITS'=>'K'); +Index: libpdl-io-hdf5-perl-0.73/t/group.t +=================================================================== +--- libpdl-io-hdf5-perl-0.73.orig/t/group.t ++++ libpdl-io-hdf5-perl-0.73/t/group.t +@@ -78,7 +78,7 @@ my $dataset = new PDL::IO::HDF5::Dataset + my $pdl = sequence(5,4); + + +-ok( $dataset->set($pdl) ); ++ok( $dataset->set($pdl, unlimited => 1) ); + # print "pdl written = \n".$pdl."\n"; + + +Index: libpdl-io-hdf5-perl-0.73/t/reference.t +=================================================================== +--- libpdl-io-hdf5-perl-0.73.orig/t/reference.t ++++ libpdl-io-hdf5-perl-0.73/t/reference.t +@@ -18,7 +18,7 @@ my $group=$hdf5->group('group1'); + # Store a dataset + my $dataset=$hdf5->dataset('data1'); + my $data = pdl [ 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 11.0, 12.0 ]; +-$dataset->set($data); ++$dataset->set($data, unlimited => 1); + + # create the reference + my @regionStart = ( 3 ); +Index: libpdl-io-hdf5-perl-0.73/t/total.t +=================================================================== +--- libpdl-io-hdf5-perl-0.73.orig/t/total.t ++++ libpdl-io-hdf5-perl-0.73/t/total.t +@@ -52,7 +52,7 @@ my $dataset = $hdfobj->dataset('rootdata + my $pdl = sequence(5,4); + + +-ok($dataset->set($pdl) ); ++ok($dataset->set($pdl, unlimited => 1) ); + # print "pdl written = \n".$pdl."\n"; + + # Create String dataset using PDL::Char +@@ -60,7 +60,7 @@ my $dataset2 = $hdfobj->dataset('charDat + + my $pdlChar = new PDL::Char( [ ["abccc", "def", "ghi"],["jkl", "mno", 'pqr'] ] ); + +-ok($dataset2->set($pdlChar)); ++ok($dataset2->set($pdlChar, unlimited => 1)); + + + my $pdl2 = $dataset->get; +@@ -92,7 +92,7 @@ $dataset = $subgroup->dataset('my datase + $pdl = sequence(5,4)->float; # Try a non-default data type + + +-ok( $dataset->set($pdl) ); ++ok( $dataset->set($pdl, unlimited => 1) ); + # print "pdl written = \n".$pdl."\n"; + + +@@ -119,7 +119,7 @@ $dataset = $subgroup->dataset('my datase + $pdl = sequence(5,4)->long; # Try a non-default data type + + +-ok( $dataset->set($pdl) ); ++ok( $dataset->set($pdl, unlimited => 1) ); + # print "pdl written = \n".$pdl."\n"; + + diff -Nru libpdl-io-hdf5-perl-0.73/debian/patches/series libpdl-io-hdf5-perl-0.73/debian/patches/series --- libpdl-io-hdf5-perl-0.73/debian/patches/series 2016-10-24 22:41:04.000000000 +0200 +++ libpdl-io-hdf5-perl-0.73/debian/patches/series 2018-10-22 14:58:43.000000000 +0200 @@ -4,3 +4,4 @@ reproducible_build.patch spelling-errors.patch hdf5-1.10.patch +hdf5-1.10.3.patch
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--- Begin Message ---Source: libpdl-io-hdf5-perl Source-Version: 1:0.73-5 We believe that the bug you reported is fixed in the latest version of libpdl-io-hdf5-perl, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Bas Couwenberg <[email protected]> (supplier of updated libpdl-io-hdf5-perl package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 22 Oct 2018 18:26:09 +0200 Source: libpdl-io-hdf5-perl Binary: libpdl-io-hdf5-perl Architecture: source amd64 Version: 1:0.73-5 Distribution: unstable Urgency: medium Maintainer: Debian Perl Group <[email protected]> Changed-By: Bas Couwenberg <[email protected]> Description: libpdl-io-hdf5-perl - PDL Interface to the HDF5 Data Format Closes: 911609 Changes: libpdl-io-hdf5-perl (1:0.73-5) unstable; urgency=medium . * Team upload. * Bump Standards-Version to 4.2.1, no changes. * Add patch by Gilles Filippini for HDF5 1.10.3 support. (closes: #911609) Checksums-Sha1: 39c162c84f1f6d27842d6f72a805de795181ff83 2141 libpdl-io-hdf5-perl_0.73-5.dsc 1b62c9868430f9ac19290babf4f2b45752f66181 6068 libpdl-io-hdf5-perl_0.73-5.debian.tar.xz e4eb27b9fa1d668aef814254b4e417c905f113e3 81428 libpdl-io-hdf5-perl-dbgsym_0.73-5_amd64.deb ffa31a1c85f0a7d11283cf43205f7e74bc8aedc7 7561 libpdl-io-hdf5-perl_0.73-5_amd64.buildinfo edd4dc503f5740cc4cab62cfcaab53d4bc25e7aa 53004 libpdl-io-hdf5-perl_0.73-5_amd64.deb Checksums-Sha256: 64b35ad717a898c605e4a47bd09a0fdd6b81d2951d5dfbb3231d6a2cef948478 2141 libpdl-io-hdf5-perl_0.73-5.dsc 2b8abab4d91ac9a93690f3cbad7e8cf42aaa8c997553b87a98983e68b044be78 6068 libpdl-io-hdf5-perl_0.73-5.debian.tar.xz 633012ea7018c4d76036480a192fd3680cb285e361429fa68d11f14f8b382125 81428 libpdl-io-hdf5-perl-dbgsym_0.73-5_amd64.deb d2f0612ff8d9ae56247060731d82286c1663857a4e090d45c5aed97b54e45222 7561 libpdl-io-hdf5-perl_0.73-5_amd64.buildinfo 1aa54cad8b0a285551bc17380a43575c70c61a21bb6b0bbfcee267ed58905e41 53004 libpdl-io-hdf5-perl_0.73-5_amd64.deb Files: 0d7437649e679fa5a16986d35bf61a02 2141 perl optional libpdl-io-hdf5-perl_0.73-5.dsc af4c7ade2e5ffcd708297e2e55ce69c0 6068 perl optional libpdl-io-hdf5-perl_0.73-5.debian.tar.xz 54957dcf9da2e7b83ffa5e94cb3019b3 81428 debug optional libpdl-io-hdf5-perl-dbgsym_0.73-5_amd64.deb 4051d8ba08dd4e3352c95bab18176127 7561 perl optional libpdl-io-hdf5-perl_0.73-5_amd64.buildinfo ecdfaa74f7825cfdcee436f281b6f577 53004 perl optional libpdl-io-hdf5-perl_0.73-5_amd64.deb -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEgYLeQXBWQI1hRlDRZ1DxCuiNSvEFAlvN/BUACgkQZ1DxCuiN SvGoMA//fvVsmBE29hwfDLK8y8rJbNmjs5+DUetGhUW2h+QZhxiuPLg4eps68rrb HuQ1WwVlnDfsy8z1mIAQ09rfyghf7VCzngqmhdTFxiuclI4nrXjyhSptjYcXv+Ic OOuj62f3cVJHPml27fi5LM/I5yv+2FSsWC27KclLY+2yAldzqK6J2BYIXjlyLqgi 88vTVEB4D/8b5UEimCiHazJEHiWX1PB8mhzmVGmTFgQn8kp00aeapItXwL+KLtpH 7VCWJ5y/5aApjd1R8BQ231YIdluWjJ1huFKc/6b5MKrtJUyHHKa2TfZfVnFAtR35 7XBclPWNmz5pkoGAehnj1KEeu8cX4BFIx/pOTFXl6l+CAm4ZT+b6ikEdqoneM2/4 xai/c5QlIp0MbrR2tWNEyEDODgljBSbYEOV3FCkw/veLebFc5OGUZd3xF5Wm0wn8 tQKxoGcBdRKgNFRTiJuGMIQSu5da7A0IO92pNe1Xx4hvf1ZWVlYA03VUpfC3ugDB 9B06U1Qh+MoYm/UlpIufbWxGy65LnwvxPmMAMBneiqRCRmEQu5pSYUNY3ENcOUBB J0qgx42M+zgaU0aS9lYrqBZEgQrqAdB8/lof3/zhCIotJMylgLxDggetq8KQOxil 28eyOGLVaIghPzaCVDvJBsNzyAj4w/+P9IspBbaMIwy4C+sLMWM= =F0WB -----END PGP SIGNATURE-----
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